background in biogeochemistry

Background in Biogeochemistry

Definition of Ecological Biogeochemistry--study of the biological and chemical transformations and fluxes of elements and compounds in populations, communities, ecosystems of the Earth.


Elements can be separated into reservoirs or pools and transfers among these pools are measured by fluxes. The content of the pool is controlled by fluxes in and out of the reservoirs and transformations within the reservoir. The actual delineation of reservoirs and fluxes depends on scale of measurement both with respect to time and pace.

Some definitions:

Reservoir (box, compartment)--An amount of matter or energy defined by certain physical, chemical ,or biological characteristics that, under the particular consideration, can be considered as reasonably homogenous.

Flux--The amount of matter or energy transferred from one reservoir to another per unit time.


Source--The flux of matter or energy into a reservoir.

Sink--The flux of matter or energy out of a reservoir.

Budget--A balance of all sources and sinks of a reservoir.


A mean residence time “” can be defined such that:

= amount in reservoir/sum of all fluxes (pool/mass input or mass output).

If the reservoir amount is constant, it is in steady state. The assumption of steady state is often very important and useful especially for very large reservoirs. It is very difficult to detect divergence from steady state of large reservoirs over a short period.

The analysis or depiction of the interconnections reservoirs and fluxes of a biogeochemical component is termed a cycle.


Some aspects of element composition and behavior are illustrated in Table 1.

The major elements include Si, C, Al and Ca.

T = pool/mass input or mass output

Table 1. Oxidation State, Abundance and Residence Times of Major Elements

(units of 1020 moles and 106 years)

Element Oxidation State(s) Hydrosphere(Ocean) (-H2O)

Pool T

LithospherePool T

AtmospherePool T

BiospherePool T

Total

Si +4 0.0014 0.016 220 450 220

C +4 - -4 0.033 0.088 61 0.00059

0.19 0.0042 0.078 61

Al +3 57 504 57

Ca +2 0.15 1.2 50 351 50

Mg +2 0.82 15 25 381 26

Na +1 7.1 193 125 288 22

Fe +3, +2 17 481 17

Cl -1 8.2 305 5.9 218 14

K +1 0.15 8.2 13 399 13

S +6, +4, +2, 0, -2 0.42 22 4.9 242 5.3

N +5, +4, +3, +2, +1, 0, -3 0.016 0.7 2.7 3.5

P +5 0.27 0.27

O -2, 0 0.387 0.38

Background in Biogeochemistry (cont.)

Most of the major elements are largely found in the lithosphere (solid part of the Earth including the crust and outer mantle ~ 100 km) and exhibit long residence times in this pool.

For the most part, the atmosphere (the mass of air surrounding the Earth) and biosphere (regions of the surface and atmosphere of the Earth where living organisms exist) are minor element pools.

Only for N is the atmosphere a significant pool.

For some elements, a significant fraction of the mass is found in the oceans (Na, Cl, S).

Some elements exhibit more than one oxidation state and therefore can participate in redox (oxidation-reduction) reactions (e.g. C, Fe, S, N, O).

Acid-Base Chemistry

Acid—a substance that increases [H+] in water.

Base—a substance that increases [OH-] in water.

pH = -log10 [H+] in moles L-1

For pure water at 24C: [H+] [OH-]= [10-7][10-7] = 10-14

pH = 7

pH Scale

[H + ] e q L -11 e -1 2 1 e -1 1 1 e -1 0 1 e -9 1 e -8 1 e -7 1 e -6 1 e -5 1 e -4 1 e -3 1 e -2

pH

0

2

4

6

8

1 0

1 2

1 4

L e m o n J u ic eV in e g a r

R a in & C O 2

P u re W a te r

A m m o n ia

Acid-Base Chemistry (cont.)

Major ionic solutes

Cations (positively charged ions)

Basic - Ca2+, Mg2+, K+, Na+ largely derived from cationsupply in the lithosphere

Acidic - H+, Al3+, Fe3+ occurs under acidic conditions

Reduced - Fe2+, Mn2+ occurs under reducing conditions(sediments, wetlands)


Anions (negatively charged ions)

Strong acid anions - SO42-, NO3

-, Cl- (strongly dissociated with H+)

Weak acid anions - HCO3-, CO3

2-, An- (organic anions)

Basic - OH-

CB - sum of basic cations

(often expressed in eq L-1 or molc L-1)

= 2[Ca2+] + 2[Mg2+] + [Na+] + [K+]

CA - sum of strong acid anions

= 2[SO42-] + [NO3

-] + [Cl-]


Dissolved inorganic carbon (DIC) = CT

[H2CO3*] + [HCO3

-] + [CO32-]

The distribution of inorganic carbon species is a function of pH (see figure).

H2CO3* = H+ + HCO3

- ; pKa1 = 6.3

HCO3- = H+ + CO3

2- ; pKa2 = 10.3


An important measurement of the acid-base status of waters is acid neutralizing capacity or alkalinity.

ANC = [HCO3-] + 2[CO3

2-] + n[An-] + [OH-] - [H+]

= the ability of a system to neutralize inputs of strong acid.

HCO3- + H+ = H2CO3

*

CO32- + 2H+ = H2CO3

OH- + H+ = H2O

ANC = CB - CA


An important concept is electroneutrality.

All solutions (and systems) must be electrically neutral.

ci - concentration of ionic solutezi - charge

2[Ca2+] + 2[Mg2+] + [Na+] + [K+] + [H+] = 2[SO4

2-] + [NO3-] + [Cl-] + [HCO3

-] + 2[CO32-] + n[An-] + [OH-]

Rearranging

ANC= [HCO3-] + 2[CO3

2-] + n[An-] + [OH-] - [H+]= 2[Ca2+] + 2[Mg2+] + [Na+] + [K+] - 2[SO4

2-] - [NO3-] - [Cl-]

= CB - CA

z ci ii 0


Increases in Ca2+ by weathering of minerals increases ANC.

CaCO3 + H+ = Ca2+ + HCO3-

Inputs of H2SO4 from acid rain decreases ANC.

H2SO4 = 2H+ + SO42-

Any process which affects the concentration of ionic solutes changes ANC.

There is a non-linear relationship between ANC and pH (see figure).

e.g., ANC production is an important indicator of the abiotic fixation or removal of CO2.


Weathering is an important process by which CO2 is fixed from the atmosphere.

NaAlSi3O8(s) + H2O + CO2 = Na+ + HCO3- + Al(OH)3(s) + 3H4SiO4

(albite)

This HCO3- is transported by rivers to the oceans.

A budget for bicarbonate of the ocean is shown in Table 2 (from Berner and Berner).

Present-Day Budget

Inputs Outputs

Rivers 1980 CaCO3 deposition:

Biogenic pyrite formation 145 Shallow water 1580

Deep sea 1340

Total 2125 Total 2920

Table 2. The Oceanic Bicarbonate Budget (rates in Tg HCO3- yr-1)

Budget for Past 25 Million Years

Inputs Outputs

Rivers 1980 CaCO3 deposition:

Biogenic pyrite formation 73 Shallow water 730

Deep sea 1340

Total 2053 Total 2070

Note: Tg = 1012g. Replacement time for HCO3 (river input only) is 83,000 years.


There are two budgets presented.

The first is the current budget.The second is the budget over the past 25 MY.

Note that the major inputs of HCO3- are riverine inputs and biogenic

pyrite formation. About 7% of the total HCO3- inputs is associated

with SO42- reduction.

2CH2O + SO42- = H2S + 2HCO3

-

Also remember: Ca2+ + HCO3- CaCO3 + H+

Organic Matter

Dissolved SO42-

Iron MineralsPyrite FeS2

Organic S Compounds

H2S

Ba c

ter i

a

Bacteria


The sink of HCO3- inputs to the oceans is precipitation of CaCO3.

Ocean water is not oversaturated with respect to the solubility of CaCO3 over the entire depth.

The upper waters are oversaturated while the lower waters are undersaturated.

The reason for this pattern is that the solubility of CaCO3 increases with increasing depth due to increases in pressure (see figure). Also, solubility increases with temperature. At the average ocean depth, the pressure is 400 atm. Under these conditions, CaCO3 is about twice as soluble as at the surface.

Ca HCO CaCO H O + CO2+3-

D

P

3(s) 2 2


Also, the production of CO2 from respiration of organic matter facilitates the dissolution of CaCO3.

What happens with increasing [CO2]?

About 83% of the precipitated CaCO3 redissolves at depth.

CO2 + H2O + CaCO3 = Ca2+ + HCO3-


Note that the current ocean is not at steady-state with respect to inputs of HCO3

-. Over the short-term, HCO3- is being depleted, sediment

deposition exceeds inputs. At the current rate of deposition, all of the HCO3

- in the ocean would be removed in 200,000 yr. This condition would never exist, as the ocean would eventually become undersaturated with respect to the solubility of CaCO3 and precipitation would stop.

The condition of elevated CaCO3 deposition to sediments has only been occurring during the past 11,000 yr. This condition is due to the rapid post-glacial rise of sea level over the continent of shelves.

Role of the biota: coral reefs, forminifera, etc.

Redox Chemistry

Redox reactions involve the transfer of electrons.

All redox reactions must be coupled and require an electron donor and electron acceptor.

e.g.CH2O + H2O = CO2 + 4e- + 4H+

O2 + 4e- + 4H+ = 2H2O

CH2O + O2 = CO2 + H2O

Redox reactions are often characterized in stoichiometric half reactions.

e.g. Fe3+ + e- = Fe2+

Redox Chemistry (cont.)

This reaction can be written as a mass law.

where K is a thermodynamic equilibrium constant.

If we take the logarithm of this expression.

or

pe = - log[e-] and is the indicator of the redox status of the system.oxidizing conditions - high or positive pe values (high K)reducing conditions - low or negative pe values (low K)

[Fe[Fe e

K2+

3+ -]

][ ]

log[Fe[Fe

log [e log K2+

3+-]

]]

pe = log[Fe[Fe

log K3+

2+]]


Only a few elements dominate redox reactions in natural waters.Major redox elements - C, N, O, S, Fe, Mn

The most important electron donor in natural waters is organic matter.

The electron acceptor that is coupled with the electron donor (organic matter) is variable. It depends on the quantity and energetics of the electron acceptor.

Redox reactions in the natural environment can be thought of as an electron titration. The source of electrons is the electron donor (organic matter). These electrons are released to electron acceptors in order of their electron affinity or energetics.

Log K

pe0 pe0w

Aerobic respiration ¼O2 + H+ + e- = ½H2O 20.75 13.75

Denitrification NO3- + 6/5 H+ + e- = 1/10 N2 + 3/2 H2O 21.05 12.65

Mn reduction ½MnO2(s) + 2H+ + e- = ½Mn2+ + H2O 20.8 6.8

Fe reduction Fe(OH)3(s) + 3H+ + e- = Fe2+ + 3H2O 16.0 -5.0

SO42- reduction cSO4

2- +9/8 H+ + e- = cHS- + ½H2O 4.25 -3.6

Methanogenesis cCO2(g) + H+ + e- = cCH4(g) + ¼ H2O 2.9 -4.1

peo = standard electron activity

Peow = standard electron activity in water at pH =7.0 for 25C


The energy yield of these electron acceptor reactions decreases as a function of energetic yield (electron activity). So, O2 is the preferred electron acceptor. When O2 is consumed, electrons are transferred to NO3

- and so on.

Note that when the electron acceptor O2 is in excess, conditions are aerobic (i.e. Earth's surface).

When the quantity of electron donor (organic matter) exceeds the quantity of electron acceptor (O2), then anaerobic conditions result.

These conditions occur in wetlands or in lake sediments.


If photosynthetic products were oxidized completely by respiration, the atmosphere would be devoid of O2.

Photosynthesis is a critical process in generating O2. Light energy is converted to chemical energy.

The electron cycle is responsible for the partitioning of an oxidizing atmosphere and reducing lithosphere.

Methods

Water Column Monitoring – 1981, 1989, 1990, 1991, 2000

O2

NO3-

NH4+

SO42-

(H2S)TFe2+

CH4AlkalinitypHDIC – calculated from alkalinity, pH, temperature

Sediment Traps – 10m – 1989, 1990, 1991POC

ConstituentRate (mmol m-2d-1)

Year1981 1989 1990 1991

DIC 35 32 49 42NH4

+ 5.3 11.8 10.9 10.0

O2 -62 -63 -41 -48

NO3- - -8.8 -4.7 -5.4

Fe2+ 0.9 1.6 1.1 1.6SO4

2- - -11.2 -11.0 -7.0

H2S 16.5 9.9 14.7 13.5

CH4* - 15.7 (10.5) 14.5 (9.7) 18.1 (12.1)

Rates of Solute Accumulation (+) or Loss (-) in the Hypolimnion of Onondaga Lake

* Includes ebullitive loss, assumed to be 33% of total; soluble component in parentheses.

Effective Equilibrium Constants of Aquatic Redox Couples

Reaction pe0 pe0w (pH = 7)

¼O2 + H+ + e- = ½ H2O 20.75 13.75

1/5 NO3- + 6/5 H+ + e- = 1/10 N2(g) + 3/5 H2O 21.05 12.65

½ MnO2(s) + 2H+ + e- = ½ Mn2+ + H2O 20.8 6.8

Fe(OH)3(am) + 3H+ + e- = Fe2+ + 3H2O 16 -5.01/8 SO4

2- + 5/4 H+ + e- = 1/8 H2S(g) + ½ H2O 5.25 -3.5

1/8 CO2 (g) + H+ + e- = 1/8 CH4 + ¼ H2O 2.9 -4.1

Oxygen Reduction DIC Equivalents per Mole O2: -1(CH2O)106(NH3)16H3PO4 + 106 O2 106 CO2 + 16 NH3 + H3PO4 + 106 H2O

Denitrification DIC Equivalents per Mole NO3-: -1.25

(CH2O)106(NH3)16H3PO4 + 84.9 HNO3 106 CO2 + 16 NH3 + H3PO4 + 42.4 N2 + 148.4 H2O

Manganese Reduction DIC Equivalents per Mole Mn: 0.5(CH2O)106(NH3)16H3PO4 + 212 MnO2 + 424 H+ 106 CO2 + 16 NH3 + H3PO4 + 212 Mn2+ + 318 H2O

Iron Reduction DIC Equivalents per Mole Fe2+: 0.25(CH2O)106(NH3)16H3PO4 + 424 FeOOH + 848 H+ 106 CO2 + 16 NH3 + H3PO4 + 424 Fe2+ + 742 H2O

Sulfate Reduction DIC Equivalents per Mole H2S: -2(CH2O)106(NH3)16H3PO4 + 53 SO4

2- 106 CO2 + 16 NH3 + H3PO4 + 53 S- + 106 H2O

Iron & Sulfate Reduction DIC Equivalents per Mole SO42-: -2.25

(CH2O)106(NH3)16H3PO4 + 47.1 FeOOH + 47.1 SO42- + 94.2 H+ 106 CO2 + 16 NH3 + H3PO4 + 47.1 FeS + 176.6 H2O

Methanogenesis DIC Equivalents per Mole CH4: 1(CH2O)106(NH3)16H3PO4 53 CO2 + 16 NH3 + H3PO4 + 53 CH4

Fermentation DIC Equivalents per Mole C: 0.5(CH2O)106(NH3)16H3PO4 35.3 CO2 + 16 NH3 + H3PO4 + 35.3 C2H5OH

Humification DIC Equivalents per Mole C: 0.5(CH2O)106(NH3)16H3PO4 35.3 CO2 + ( C2H5OH)35.3 (NH3)16 H3PO4

Organic Carbon Budget 1987-92

Rate(mmol C m-2 d-1)

%

Organic C Inputs (Sediment Traps) 62 100

DIC Release (Water Column) 41 66

CH4 (Water Column) 16 26

Total C Release 57 92

Net Sediment C Accumulation 5 8

Organic C Burial (Sediments) 26

Hypolimnion Electron Budget 1987-92

Rate(meq m-2d-1)

%

Electron Donor (Sediment Traps) 248 100

Electron Acceptors (Water Column)

O2 69 28

NO3- 18 7

Fe3+ 0.79 <1

SO42- 49 20

CH4 41 16

Total Electron Acceptors Measured 178 72

Net Electron Transfer to Sediments 70 28

Net Electron Burial in Sediments (Sediments) 105

Comparison of Hypolimnetic Electron Budgets During Summer Stratification

Lake

Fluxes Electron Donor

(meq m2d-1)

Fluxes Electron Acceptors (meq m-2 d-1)

O2 NO3- Fe3+ SO4

2- CH4 Total

Bleltham Tarm 154 18 (49) 7.3 (20) ND 0.85 (2) 10.7 (29) 36.8

Dart’s 18.8 15.2 (81) 2.8 (14) 0.4 (2) 0.7 (4) - 18.8

Mirror 40 9.2 (69) 0 (0) 0.43 (3) 1.5 (20) 2.3 (17) 13.4

L226 ND 15.2 (30) 4.2 (8) 0.97 (2) 8.1 (16) 23 (45) 51.8

L227 84 1.6 (5) 0.3 (1) 0.6 (2) 8.8 (28) 20.1 (64) 31.3

L223 ND 2.7 (10) 0.3 (1) 1.8 (7) 9.1 (34) 12.8 (48) 26.8

Onondaga Lake 1989-91 240 69 (39) 18 (10) 0.79 (<1) 49 (27) 41 (23) 178

background in biogeochemistry

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